Nuclear sequences of mitochondrial origin in domestic yak.

Mitochondrial DNA sequences are frequently transferred into the nuclear genome, generating nuclear mitochondrial DNA sequences (NUMTs). Here, we analysed, for the first time, NUMTs in the domestic yak genome. We obtained 499 alignment matches covering 340.2 kbp of the yak nuclear genome. After a merging step, we identified 167 NUMT regions with a total length of ~ 503 kbp, representing 0.02% of the nuclear genome. We discovered copies of all mitochondrial regions and found that most NUMT regions are intergenic or intronic and mostly untranscribed. 98 different NUMT regions from domestic yak showed high homology with cow and/or wild yak genomes, suggesting selection or hybridization between domestic/wild yak and cow. To rule out the possibility that the identified NUMTs could be artifacts of the domestic yak genome assembly, we validated experimentally five NUMT regions by PCR amplification. As NUMT regions show high similarity to the mitochondrial genome can potentially pose a risk to domestic yak DNA mitochondrial studies, special care is therefore needed to select primers for PCR amplification of mitochondrial DNA sequences.

Survey of mitochondrial sequences integrated into the bovine nuclear genome.

Nuclear copies of the mitochondrial DNA (NUMTs) have already been described in several species. In this context, we identified and analysed 166 bovine NUMT regions with a total length of 430 kbp, representing about 0.02% of the cattle nuclear genome. Copies of all mitochondrial regions were detected in the nuclear genome, with distinct degrees of sequence similarity to the mitogenome. Some NUMT regions include large mitogenome segments and show high similarity to the organelle genome sequence. NUMT regions are frequently modified by insertion of repetitive sequences and by sequence rearrangements. We confirmed the existence of 29 NUMT regions by PCR amplification using DNA from the cow (Dominette) which was used to generate the bovine genome reference sequence, ruling out the possibility that these NUMTs could be artifacts of the genome assembly. As there are NUMT regions with high similarity to the mitogenome, special care is needed when designing primers for mitochondrial DNA amplification. Our results can therefore be used to avoid co-amplification of bovine nuclear sequences similar to mitochondrial DNA.